Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/m/mdtraj/mdtraj_1.9.5-1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/mdtraj-1.9.5-1_3ftcfdj/mdtraj_1.9.5-1_amd64.buildinfo Get source package info: mdtraj=1.9.5-1 Source URL: http://snapshot.notset.fr/mr/package/mdtraj/1.9.5-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-14 automake=1:1.16.3-2 autopoint=0.21-3 autotools-dev=20180224.1+nmu1 base-files=11 base-passwd=3.5.48 bash=5.1-2 binutils=2.35.1-7 binutils-common=2.35.1-7 binutils-x86-64-linux-gnu=2.35.1-7 bsdextrautils=2.36.1-6 bsdutils=1:2.36.1-5 build-essential=12.9 bzip2=1.0.8-4 ca-certificates=20200601 coreutils=8.32-4+b1 cpp=4:10.2.1-1 cpp-10=10.2.1-6 cython3=0.29.21-3+b1 dash=0.5.11+git20200708+dd9ef66-5 debconf=1.5.74 debhelper=13.3.1 debianutils=4.11.2 dh-autoreconf=19 dh-python=4.20201102 dh-strip-nondeterminism=1.9.0-1 diffutils=1:3.7-5 docutils-common=0.16+dfsg-3 dpkg=1.20.7.1 dpkg-dev=1.20.7.1 dwz=0.13+20201015-2 file=1:5.39-3 findutils=4.8.0-1 fonts-mathjax=2.7.9+dfsg-1 g++=4:10.2.1-1 g++-10=10.2.1-6 gcc=4:10.2.1-1 gcc-10=10.2.1-6 gcc-10-base=10.2.1-6 gettext=0.21-3 gettext-base=0.21-3 grep=3.6-1 groff-base=1.22.4-5 gzip=1.10-2 hostname=3.23 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-9 libaec0=1.0.4-1 libarchive-zip-perl=1.68-1 libasan6=10.2.1-6 libatomic1=10.2.1-6 libattr1=1:2.4.48-6 libaudit-common=1:3.0-2 libaudit1=1:3.0-2 libbinutils=2.35.1-7 libblas3=3.9.0-3 libblkid1=2.36.1-5 libblosc1=1.20.1+ds1-2 libbz2-1.0=1.0.8-4 libc-bin=2.31-9 libc-dev-bin=2.31-9 libc6=2.31-9 libc6-dev=2.31-9 libcap-ng0=0.7.9-2.2+b1 libcc1-0=10.2.1-6 libcom-err2=1.45.6-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.1-7 libctf0=2.35.1-7 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.256 libdebhelper-perl=13.3.1 libdpkg-perl=1.20.7.1 libelf1=0.182-3 libexpat1=2.2.10-1 libexpat1-dev=2.2.10-1 libffi7=3.3-5 libfile-stripnondeterminism-perl=1.9.0-1 libgcc-10-dev=10.2.1-6 libgcc-s1=10.2.1-6 libgcrypt20=1.8.7-2 libgdbm-compat4=1.19-1 libgdbm6=1.19-1 libgfortran5=10.2.1-6 libgmp10=2:6.2.1+dfsg-1 libgomp1=10.2.1-6 libgpg-error0=1.38-2 libgssapi-krb5-2=1.18.3-4 libhdf5-103-1=1.10.6+repack-2 libicu67=67.1-6 libisl23=0.23-1 libitm1=10.2.1-6 libjs-jquery=3.5.1+dfsg+~3.5.5-7 libjs-mathjax=2.7.9+dfsg-1 libjs-sphinxdoc=3.4.3-1 libjs-underscore=1.9.1~dfsg-1 libk5crypto3=1.18.3-4 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-4 libkrb5support0=1.18.3-4 liblapack3=3.9.0-3 liblbfgsb0=3.0+dfsg.3-9 liblsan0=10.2.1-6 liblz4-1=1.9.3-1 liblzma5=5.2.5-1.0 liblzo2-2=2.10-2 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmount1=2.36.1-5 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libncursesw6=6.2+20201114-2 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libpam-modules=1.4.0-2 libpam-modules-bin=1.4.0-2 libpam-runtime=1.4.0-2 libpam0g=1.4.0-2 libpcre2-8-0=10.36-2 libpcre3=2:8.39-13 libperl5.32=5.32.0-6 libpipeline1=1.5.3-1 libpython3-all-dev=3.9.1-1 libpython3-dev=3.9.1-1 libpython3-stdlib=3.9.1-1 libpython3.9=3.9.1-2 libpython3.9-dev=3.9.1-2 libpython3.9-minimal=3.9.1-2 libpython3.9-stdlib=3.9.1-2 libquadmath0=10.2.1-6 libreadline8=8.1-1 libseccomp2=2.5.1-1 libselinux1=3.1-2+b2 libsigsegv2=2.12-3 libsmartcols1=2.36.1-5 libsnappy1v5=1.1.8-1 libsqlite3-0=3.34.0-1 libssl1.1=1.1.1i-1 libstdc++-10-dev=10.2.1-6 libstdc++6=10.2.1-6 libsub-override-perl=0.09-2 libsystemd0=247.2-4 libsz2=1.0.4-1 libtinfo6=6.2+20201114-2 libtirpc-common=1.3.1-1 libtirpc-dev=1.3.1-1 libtirpc3=1.3.1-1 libtool=2.4.6-15 libtsan0=10.2.1-6 libubsan1=10.2.1-6 libuchardet0=0.0.7-1 libudev1=247.2-4 libunistring2=0.9.10-4 libuuid1=2.36.1-5 libxml2=2.9.10+dfsg-6.3+b1 libzstd1=1.4.8+dfsg-1 linux-libc-dev=5.10.5-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-5 mailcap=3.68 make=4.3-4 man-db=2.9.3-2 mawk=1.3.4.20200120-2 media-types=4.0.0 mime-support=3.66 ncurses-base=6.2+20201114-2 ncurses-bin=6.2+20201114-2 openssl=1.1.1i-1 patch=2.7.6-7 perl=5.32.0-6 perl-base=5.32.0-6 perl-modules-5.32=5.32.0-6 po-debconf=1.0.21+nmu1 python-babel-localedata=2.8.0+dfsg.1-5 python-tables-data=3.6.1-3 python3=3.9.1-1 python3-alabaster=0.7.8-1.1 python3-all=3.9.1-1 python3-all-dev=3.9.1-1 python3-astor=0.8.1-1 python3-babel=2.8.0+dfsg.1-5 python3-certifi=2020.6.20-1 python3-chardet=4.0.0-1 python3-dateutil=2.8.1-5 python3-decorator=4.4.2-2 python3-dev=3.9.1-1 python3-distutils=3.9.1-2 python3-docutils=0.16+dfsg-3 python3-idna=2.10-1 python3-imagesize=1.2.0-2 python3-jinja2=2.11.2-1 python3-lib2to3=3.9.1-2 python3-markupsafe=1.1.1-1+b3 python3-minimal=3.9.1-1 python3-networkx=2.5+ds-2 python3-numexpr=2.7.2-1 python3-numpy=1:1.19.5-1 python3-packaging=20.8-1 python3-pandas=1.1.5+dfsg-2 python3-pandas-lib=1.1.5+dfsg-2 python3-pkg-resources=51.1.0-1 python3-pygments=2.7.1+dfsg-1 python3-pyparsing=2.4.7-1 python3-requests=2.25.1+dfsg-2 python3-roman=2.0.0-5 python3-scipy=1.6.0-2 python3-setuptools=51.1.0-1 python3-six=1.15.0-2 python3-snowballstemmer=2.0.0-2 python3-sphinx=3.4.3-1 python3-tables=3.6.1-3 python3-tables-lib=3.6.1-3 python3-tz=2020.5-1 python3-urllib3=1.26.2-1 python3.9=3.9.1-2 python3.9-dev=3.9.1-2 python3.9-minimal=3.9.1-2 readline-common=8.1-1 sed=4.7-1 sensible-utils=0.0.14 sgml-base=1.30 sphinx-common=3.4.3-1 sysvinit-utils=2.96-5 tar=1.32+dfsg-1 tzdata=2020f-1 util-linux=2.36.1-5 xml-core=0.18+nmu1 xz-utils=5.2.5-1.0 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210207T151314Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20210117T204310Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d mdtraj=1.9.5-1 && mkdir -p /build/mdtraj-04fkzS && dpkg-source --no-check -x /*.dsc /build/mdtraj-04fkzS/mdtraj-1.9.5 && chown -R builduser:builduser /build/mdtraj-04fkzS" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/mdtraj-04fkzS/mdtraj-1.9.5 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1610947854" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/mdtraj-04fkzS /tmp/mdtraj-1.9.5-1_3ftcfdj bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20210117T204310Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.jBkHI0i_TA as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.jBkHI0i_TA Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-5). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20210117T204310Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210117T204310Z unstable/main amd64 fakeroot amd64 1.25.3-1.1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (849 kB/s) Selecting previously unselected package libfakeroot:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4661 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ... Unpacking fakeroot (1.25.3-1.1) ... Setting up libfakeroot:amd64 (1.25.3-1.1) ... Setting up fakeroot (1.25.3-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-9) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210207T151314Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20210117T204310Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.jBkHI0i_TA Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210207T151314Z unstable InRelease [153 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20210117T204310Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20210207T151314Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20210207T151314Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20210207T151314Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20210207T151314Z unstable/main amd64 Packages [11.7 MB] Fetched 34.4 MB in 31s (1118 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.jBkHI0i_TA I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d mdtraj=1.9.5-1 && mkdir -p /build/mdtraj-04fkzS && dpkg-source --no-check -x /*.dsc /build/mdtraj-04fkzS/mdtraj-1.9.5 && chown -R builduser:builduser /build/mdtraj-04fkzS"' exec /tmp/mmdebstrap.jBkHI0i_TA Reading package lists... NOTICE: 'mdtraj' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/debichem-team/mdtraj.git Please use: git clone https://salsa.debian.org/debichem-team/mdtraj.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 21.8 MB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main mdtraj 1.9.5-1 (dsc) [2592 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main mdtraj 1.9.5-1 (tar) [21.5 MB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main mdtraj 1.9.5-1 (diff) [296 kB] Fetched 21.8 MB in 17s (1254 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'mdtraj_1.9.5-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting mdtraj in /build/mdtraj-04fkzS/mdtraj-1.9.5 dpkg-source: info: unpacking mdtraj_1.9.5.orig.tar.gz dpkg-source: info: unpacking mdtraj_1.9.5-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying build_dir_pybuild.patch dpkg-source: info: applying python_hashbang.patch dpkg-source: info: applying test_gsd_skip.patch dpkg-source: info: applying check_sse2.patch dpkg-source: info: applying reinstate_astor_not_astunparse_revert_a8b2b9c.patch dpkg-source: info: applying 32bit_skip_image_molecule.patch dpkg-source: info: applying test_order_relax_tol.patch dpkg-source: info: applying rename-mdconvert-mdtraj.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/mdtraj-04fkzS/mdtraj-1.9.5 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1610947854" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.jBkHI0i_TA dpkg-buildpackage: info: source package mdtraj dpkg-buildpackage: info: source version 1.9.5-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Drew Parsons dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from mdtraj-1.9.5/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ fakeroot debian/rules clean dh clean --with python3,sphinxdoc --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/mdtraj-04fkzS/mdtraj-1.9.5' dh_auto_clean || /bin/true I: pybuild base:232: python3.9 setup.py clean Using built-in specs. COLLECT_GCC=/usr/bin/x86_64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/10/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa:hsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-10-Km9U7s/gcc-10-10.2.1/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-Km9U7s/gcc-10-10.2.1/debian/tmp-gcn/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-mutex Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20210110 (Debian 10.2.1-6) ./basesetup.py:431: UserWarning: Unrecognized setuptools command ('clean'), proceeding with generating Cython sources and expanding templates warnings.warn("Unrecognized setuptools command ('{}'), proceeding with " warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. C compiler: Attempting to autodetect OpenMP support... Compiler supports OpenMP Attempting to autodetect SSE3 support... Compiler supports SSE3 Attempting to autodetect SSE4.1 support... Compiler supports SSE4.1 Attempting to autodetect NEON support... Did not detect NEON support Compiling mdtraj/formats/xtc/xtc.pyx because it changed. Compiling mdtraj/formats/xtc/trr.pyx because it changed. Compiling mdtraj/formats/tng/tng.pyx because it changed. Compiling mdtraj/formats/dcd/dcd.pyx because it changed. Compiling mdtraj/formats/binpos/binpos.pyx because it changed. Compiling mdtraj/formats/dtr/dtr.pyx because it changed. Compiling mdtraj/rmsd/_rmsd.pyx because it changed. Compiling mdtraj/rmsd/_lprmsd.pyx because it changed. Compiling mdtraj/geometry/src/_geometry.pyx because it changed. Compiling mdtraj/geometry/drid.pyx because it changed. Compiling mdtraj/geometry/neighbors.pyx because it changed. Compiling mdtraj/geometry/neighborlist.pyx because it changed. [ 1/12] Cythonizing mdtraj/formats/binpos/binpos.pyx [ 2/12] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 3/12] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 4/12] Cythonizing mdtraj/formats/tng/tng.pyx [ 5/12] Cythonizing mdtraj/formats/xtc/trr.pyx [ 6/12] Cythonizing mdtraj/formats/xtc/xtc.pyx [ 7/12] Cythonizing mdtraj/geometry/drid.pyx [ 8/12] Cythonizing mdtraj/geometry/neighborlist.pyx [ 9/12] Cythonizing mdtraj/geometry/neighbors.pyx [10/12] Cythonizing mdtraj/geometry/src/_geometry.pyx [11/12] Cythonizing mdtraj/rmsd/_lprmsd.pyx [12/12] Cythonizing mdtraj/rmsd/_rmsd.pyx running clean removing '/build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.9' does not exist -- can't clean it for f in mdtraj/formats/binpos/binpos.c \ mdtraj/formats/dcd/dcd.c \ mdtraj/formats/dtr/dtr.cpp \ mdtraj/formats/tng/tng.c \ mdtraj/formats/xtc/trr.c \ mdtraj/formats/xtc/xtc.c \ mdtraj/geometry/drid.cpp \ mdtraj/geometry/neighborlist.cpp \ mdtraj/geometry/neighbors.cpp \ mdtraj/geometry/src/_geometry.cpp \ mdtraj/rmsd/_lprmsd.cpp \ mdtraj/rmsd/_rmsd.cpp \ mdtraj/version.py; \ do rm -f $f; done rm -rf __pycache__ make[1]: Leaving directory '/build/mdtraj-04fkzS/mdtraj-1.9.5' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules build-arch dh build-arch --with python3,sphinxdoc --buildsystem=pybuild dh_update_autotools_config -a -O--buildsystem=pybuild dh_autoreconf -a -O--buildsystem=pybuild dh_auto_configure -a -O--buildsystem=pybuild I: pybuild base:232: python3.9 setup.py config Using built-in specs. COLLECT_GCC=/usr/bin/x86_64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/10/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa:hsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-10-Km9U7s/gcc-10-10.2.1/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-Km9U7s/gcc-10-10.2.1/debian/tmp-gcn/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-mutex Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20210110 (Debian 10.2.1-6) ./basesetup.py:431: UserWarning: Unrecognized setuptools command ('config'), proceeding with generating Cython sources and expanding templates warnings.warn("Unrecognized setuptools command ('{}'), proceeding with " warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. C compiler: Attempting to autodetect OpenMP support... Compiler supports OpenMP Attempting to autodetect SSE3 support... Compiler supports SSE3 Attempting to autodetect SSE4.1 support... Compiler supports SSE4.1 Attempting to autodetect NEON support... Did not detect NEON support Compiling mdtraj/formats/xtc/xtc.pyx because it changed. Compiling mdtraj/formats/xtc/trr.pyx because it changed. Compiling mdtraj/formats/tng/tng.pyx because it changed. Compiling mdtraj/formats/dcd/dcd.pyx because it changed. Compiling mdtraj/formats/binpos/binpos.pyx because it changed. Compiling mdtraj/formats/dtr/dtr.pyx because it changed. Compiling mdtraj/rmsd/_rmsd.pyx because it changed. Compiling mdtraj/rmsd/_lprmsd.pyx because it changed. Compiling mdtraj/geometry/src/_geometry.pyx because it changed. Compiling mdtraj/geometry/drid.pyx because it changed. Compiling mdtraj/geometry/neighbors.pyx because it changed. Compiling mdtraj/geometry/neighborlist.pyx because it changed. [ 1/12] Cythonizing mdtraj/formats/binpos/binpos.pyx [ 2/12] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 3/12] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 4/12] Cythonizing mdtraj/formats/tng/tng.pyx [ 5/12] Cythonizing mdtraj/formats/xtc/trr.pyx [ 6/12] Cythonizing mdtraj/formats/xtc/xtc.pyx [ 7/12] Cythonizing mdtraj/geometry/drid.pyx [ 8/12] Cythonizing mdtraj/geometry/neighborlist.pyx [ 9/12] Cythonizing mdtraj/geometry/neighbors.pyx [10/12] Cythonizing mdtraj/geometry/src/_geometry.pyx [11/12] Cythonizing mdtraj/rmsd/_lprmsd.pyx [12/12] Cythonizing mdtraj/rmsd/_rmsd.pyx running config dh_auto_build -a -O--buildsystem=pybuild I: pybuild base:232: /usr/bin/python3 setup.py build Using built-in specs. COLLECT_GCC=/usr/bin/x86_64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/10/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa:hsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-10-Km9U7s/gcc-10-10.2.1/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-Km9U7s/gcc-10-10.2.1/debian/tmp-gcn/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-mutex Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20210110 (Debian 10.2.1-6) C compiler: Attempting to autodetect OpenMP support... Compiler supports OpenMP Attempting to autodetect SSE3 support... Compiler supports SSE3 Attempting to autodetect SSE4.1 support... Compiler supports SSE4.1 Attempting to autodetect NEON support... Did not detect NEON support running build running build_py creating /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj copying mdtraj/__init__.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj copying mdtraj/io.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj copying mdtraj/version.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj creating /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/__init__.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/shift_wrappers.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/scalar_couplings.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/nmr creating /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/testing copying mdtraj/testing/testing.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/testing copying mdtraj/testing/__init__.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/testing copying mdtraj/testing/docstrings.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/testing copying mdtraj/testing/docscrape.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/testing creating /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/netcdfreporter.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/basereporter.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/__init__.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/xtcreporter.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/dcdreporter.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/hdf5reporter.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters creating /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils copying mdtraj/utils/six.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils copying mdtraj/utils/singleton.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils copying mdtraj/utils/rotation.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils copying mdtraj/utils/zipped.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils copying mdtraj/utils/__init__.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils copying mdtraj/utils/unitcell.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils copying mdtraj/utils/contextmanagers.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils copying mdtraj/utils/validation.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils copying mdtraj/utils/delay_import.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils creating /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core copying mdtraj/core/residue_names.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core copying mdtraj/core/__init__.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core copying mdtraj/core/topology.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core copying mdtraj/core/element.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core copying mdtraj/core/trajectory.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core copying mdtraj/core/selection.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core creating /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/prmtop.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/__init__.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/registry.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/mol2.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/hdf5.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/psf.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/gro.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/lammpstrj.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/netcdf.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/amberrst.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/mdcrd.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/arc.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/openmmxml.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/hoomdxml.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/xyzfile.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/gsd.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats copying mdtraj/formats/lh5.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats creating /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/contact.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/__init__.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/sasa.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/dihedral.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/internal.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/alignment.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/dssp.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/thermodynamic_properties.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/angle.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/shape.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/rdf.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/order.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/hbond.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/distance.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/rg.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry creating /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/__init__.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/mdconvert.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/mdinspect.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/scripts creating /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/baseunit.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/standard_dimensions.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/__init__.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/mymatrix.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/prefix.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_math.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/doctests.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/constants.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_operators.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/quantity.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_definitions.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/basedimension.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit creating /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbstructure.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/__init__.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbfile.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb creating /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/pdbNames.xml -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/residues.xml -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb/data running build_ext building 'mdtraj.formats.xtc' extension creating build creating build/temp.linux-x86_64-3.9 creating build/temp.linux-x86_64-3.9/mdtraj creating build/temp.linux-x86_64-3.9/mdtraj/formats creating build/temp.linux-x86_64-3.9/mdtraj/formats/xtc creating build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: mdtraj/formats/xtc/src/xdrfile.c:788:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 788 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:785:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 785 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: mdtraj/formats/xtc/src/xdrfile.c:1016:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 1016 | int errval=1; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’: mdtraj/formats/xtc/src/xdrfile.c:1305:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 1305 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:1302:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 1302 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: mdtraj/formats/xtc/src/xdrfile.c:1509:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 1509 | int errval=1; | ^~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘xtc_coord’: mdtraj/formats/xtc/src/xdrfile_xtc.c:66:8: warning: unused variable ‘j’ [-Wunused-variable] 66 | int i,j,result; | ^ mdtraj/formats/xtc/src/xdrfile_xtc.c:66:6: warning: unused variable ‘i’ [-Wunused-variable] 66 | int i,j,result; | ^ mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘read_xtc_nframes’: mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 119 | if (NULL == xd) | ^~ mdtraj/formats/xtc/src/xdrfile_xtc.c:122:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 122 | do { | ^~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from mdtraj/formats/xtc/xtc.c:639: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write’: mdtraj/formats/xtc/xtc.c:553:40: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 553 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:9374:7: note: ‘__pyx_v_status’ was declared here 9374 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read’: mdtraj/formats/xtc/xtc.c:7893:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 7893 | } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:7889:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 7889 | } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:7885:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 7885 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:7845:23: warning: ‘__pyx_pybuffernd_time_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 7845 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:7827:23: warning: ‘__pyx_pybuffernd_step_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 7827 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:7903:23: warning: ‘__pyx_pybuffernd_prec_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 7903 | } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:7865:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 7865 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:7861:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 7861 | } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:7857:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 7857 | } else if (unlikely(__pyx_t_32 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:7480:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 7480 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:7476:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 7476 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_6 = 0; | ^ x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/xtc.o -o /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/xtc.cpython-39-x86_64-linux-gnu.so building 'mdtraj.formats.trr' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: mdtraj/formats/xtc/src/xdrfile.c:788:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 788 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:785:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 785 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: mdtraj/formats/xtc/src/xdrfile.c:1016:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 1016 | int errval=1; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’: mdtraj/formats/xtc/src/xdrfile.c:1305:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 1305 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:1302:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 1302 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: mdtraj/formats/xtc/src/xdrfile.c:1509:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 1509 | int errval=1; | ^~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from mdtraj/formats/xtc/trr.c:639: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ mdtraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write’: mdtraj/formats/xtc/trr.c:553:40: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 553 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:10906:7: note: ‘__pyx_v_status’ was declared here 10906 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read’: mdtraj/formats/xtc/trr.c:8259:19: warning: ‘__pyx_pybuffernd_forces.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 8259 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:8255:19: warning: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 8255 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:1775:90: warning: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1775 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:6796:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ was declared here 6796 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8251:19: warning: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 8251 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_forces.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:8202:19: warning: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 8202 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:8198:19: warning: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 8198 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:1775:90: warning: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1775 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:6812:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ was declared here 6812 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8194:19: warning: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 8194 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_vel.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:8592:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 8592 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:8588:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 8588 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:8433:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 8433 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:8429:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 8429 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:8485:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 8485 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:8481:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 8481 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/trr.o -o /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/trr.cpython-39-x86_64-linux-gnu.so building 'mdtraj.formats.tng' extension creating build/temp.linux-x86_64-3.9/mdtraj/formats/tng creating build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src creating build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression creating build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/lib x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/bwlzh.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/bwlzh.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/bwt.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/bwt.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/coder.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/coder.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/dict.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/dict.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/fixpoint.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/fixpoint.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/huffman.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/huffman.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/huffmem.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/huffmem.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/lz77.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/lz77.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/merge_sort.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/merge_sort.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/mtf.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/mtf.o mdtraj/formats/tng/src/compression/mtf.c: In function ‘Ptngc_comp_conv_to_mtf’: mdtraj/formats/tng/src/compression/mtf.c:196:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 196 | while (dict[ptr]!=v) | ^~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/rle.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/rle.o mdtraj/formats/tng/src/compression/rle.c: In function ‘Ptngc_comp_conv_to_rle’: mdtraj/formats/tng/src/compression/rle.c:56:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 56 | if (v==vals[i]) | ^~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/tng_compress.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/tng_compress.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/vals16.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/vals16.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/warnmalloc.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/warnmalloc.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/widemuldiv.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/widemuldiv.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/xtc2.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/xtc2.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/xtc3.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/xtc3.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/lib/md5.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/lib/md5.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/lib/tng_io.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/lib/tng_io.o mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_block_header_read’: mdtraj/formats/tng/src/lib/tng_io.c:1064:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types] 1064 | tng_data->input_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:1073:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long unsigned int *)’} [-Wincompatible-pointer-types] 1073 | tng_data->input_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:1089:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types] 1089 | tng_data->input_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:1098:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long unsigned int *)’} [-Wincompatible-pointer-types] 1098 | tng_data->input_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_output_file_endianness_get’: mdtraj/formats/tng/src/lib/tng_io.c:9565:53: warning: comparison of distinct pointer types lacks a cast 9565 | if(tng_data->output_endianness_swap_func_32 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c:9570:58: warning: comparison of distinct pointer types lacks a cast 9570 | else if(tng_data->output_endianness_swap_func_32 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c:9588:53: warning: comparison of distinct pointer types lacks a cast 9588 | if(tng_data->output_endianness_swap_func_64 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c:9593:58: warning: comparison of distinct pointer types lacks a cast 9593 | else if(tng_data->output_endianness_swap_func_64 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_output_file_endianness_set’: mdtraj/formats/tng/src/lib/tng_io.c:9651:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types] 9651 | tng_data->output_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:9660:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long unsigned int *)’} [-Wincompatible-pointer-types] 9660 | tng_data->output_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:9673:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types] 9673 | tng_data->output_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:9682:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long unsigned int *)’} [-Wincompatible-pointer-types] 9682 | tng_data->output_endianness_swap_func_64 = | ^ In file included from /usr/include/string.h:495, from mdtraj/formats/tng/include/tng/tng_io.h:302, from mdtraj/formats/tng/src/lib/tng_io.c:20: In function ‘strncpy’, inlined from ‘tng_gen_data_block_add’ at mdtraj/formats/tng/src/lib/tng_io.c:12613:9: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_gen_data_block_add’: mdtraj/formats/tng/src/lib/tng_io.c:12613:47: note: length computed here 12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1); | ^~~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_data_block_write.isra’: mdtraj/formats/tng/src/lib/tng_io.c:5986:72: warning: ‘num_first_particle’ may be used uninitialized in this function [-Wmaybe-uninitialized] 5986 | for(j = num_first_particle; j < num_first_particle + n_particles; | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c:4308:24: warning: ‘n_particles’ may be used uninitialized in this function [-Wmaybe-uninitialized] 4308 | dest = tng_compress_pos_float((float *)*data, (int)n_particles, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4309 | (int)n_frames, | ~~~~~~~~~~~~~~ 4310 | f_precision, | ~~~~~~~~~~~~ 4311 | 0, alt_algo, | ~~~~~~~~~~~~ 4312 | &compressed_len); | ~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c:5684:13: note: ‘n_particles’ was declared here 5684 | int64_t n_particles, num_first_particle, n_frames, stride_length; | ^~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/tng.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/tng.o In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from mdtraj/formats/tng/tng.c:665: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ mdtraj/formats/tng/tng.c: In function ‘__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile___cinit__’: mdtraj/formats/tng/tng.c:3541:104: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 3541 | __pyx_t_1 = ((tng_util_trajectory_open(__pyx_v_filename, __pyx_v_self->mode, (&__pyx_v_self->_traj)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:3596:88: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 3596 | __pyx_t_1 = ((tng_num_particles_get(__pyx_v_self->_traj, (&__pyx_v_self->n_atoms)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:3628:90: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 3628 | __pyx_t_1 = ((tng_num_frames_get(__pyx_v_self->_traj, (&__pyx_v_self->tot_n_frames)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:3660:95: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 3660 | __pyx_t_1 = ((tng_distance_unit_exponential_get(__pyx_v_self->_traj, (&__pyx_v_exponent)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:3730:113: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 3730 | __pyx_t_1 = ((tng_num_frames_per_frame_set_get(__pyx_v_self->_traj, (&__pyx_v_self->_frames_per_frame_set)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:3774:77: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 3774 | __pyx_t_1 = ((tng_last_program_name_set(__pyx_v_self->_traj, __pyx_t_8) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c: In function ‘__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_8_read_topology’: mdtraj/formats/tng/tng.c:4568:106: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 4568 | __pyx_t_7 = ((tng_chain_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:4613:108: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 4613 | __pyx_t_7 = ((tng_residue_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:4720:115: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 4720 | __pyx_t_8 = ((tng_global_residue_id_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, (&__pyx_v_residue_id)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:4750:105: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 4750 | __pyx_t_8 = ((tng_atom_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:4878:105: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 4878 | __pyx_t_8 = ((tng_atom_type_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:5479:126: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 5479 | __pyx_t_7 = ((tng_molsystem_bonds_get(__pyx_v_self->_traj, (&__pyx_v_n_bonds), (&__pyx_v_from_atoms), (&__pyx_v_to_atoms)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c: In function ‘__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_10_read_frame’: mdtraj/formats/tng/tng.c:5887:152: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 5887 | __pyx_t_1 = ((tng_util_pos_read_range(__pyx_v_self->_traj, __pyx_v_self->_pos, __pyx_v_self->_pos, (&__pyx_v_positions), (&__pyx_v_stride_length)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:6155:108: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 6155 | __pyx_t_1 = ((tng_util_time_of_frame_get(__pyx_v_self->_traj, __pyx_v_self->_pos, (&__pyx_v_frame_time)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:6257:304: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 6257 | __pyx_t_1 = ((tng_data_vector_interval_get(__pyx_v_self->_traj, __pyx_v_6mdtraj_7formats_3tng_TNG_TRAJ_BOX_SHAPE, __pyx_v_self->_pos, __pyx_v_self->_pos, __pyx_e_6mdtraj_7formats_3tng_TNG_USE_HASH, (&__pyx_v_box_shape), (&__pyx_v_stride_length), (&__pyx_v_n_values_per_frame), (&__pyx_v_data_type)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c: In function ‘__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_16write’: mdtraj/formats/tng/tng.c:8747:94: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 8747 | __pyx_t_1 = ((tng_implicit_num_particles_set(__pyx_v_self->_traj, __pyx_v_self->n_atoms) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:8779:75: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 8779 | __pyx_t_1 = ((tng_util_pos_write_interval_set(__pyx_v_self->_traj, 1) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:8811:81: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 8811 | __pyx_t_1 = ((tng_util_box_shape_write_interval_set(__pyx_v_self->_traj, 1) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:9134:77: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 9134 | __pyx_t_9 = ((tng_time_per_frame_set(__pyx_v_self->_traj, __pyx_t_15) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:9325:372: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 9325 | __pyx_t_1 = ((tng_util_pos_write(__pyx_v_self->_traj, __pyx_v_self->tot_n_frames, (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_xyz_array.rcbuffer->pybuffer.buf, __pyx_t_18, __pyx_pybuffernd_xyz_array.diminfo[0].strides, __pyx_t_19, __pyx_pybuffernd_xyz_array.diminfo[1].strides, __pyx_t_20, __pyx_pybuffernd_xyz_array.diminfo[2].strides)))) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:9377:378: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 9377 | __pyx_t_1 = ((tng_util_box_shape_write(__pyx_v_self->_traj, __pyx_v_self->tot_n_frames, (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_box_array.rcbuffer->pybuffer.buf, __pyx_t_20, __pyx_pybuffernd_box_array.diminfo[0].strides, __pyx_t_19, __pyx_pybuffernd_box_array.diminfo[1].strides, __pyx_t_18, __pyx_pybuffernd_box_array.diminfo[2].strides)))) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:9439:89: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 9439 | __pyx_t_1 = ((tng_frame_set_first_frame_time_set(__pyx_v_self->_traj, __pyx_t_15) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/bwlzh.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/bwt.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/coder.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/dict.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/fixpoint.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/huffman.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/huffmem.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/lz77.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/merge_sort.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/mtf.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/rle.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/tng_compress.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/vals16.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/warnmalloc.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/widemuldiv.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/xtc2.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/xtc3.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/lib/md5.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/lib/tng_io.o build/temp.linux-x86_64-3.9/mdtraj/formats/tng/tng.o -lz -o /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/tng.cpython-39-x86_64-linux-gnu.so building 'mdtraj.formats.dcd' extension creating build/temp.linux-x86_64-3.9/mdtraj/formats/dcd creating build/temp.linux-x86_64-3.9/mdtraj/formats/dcd/src x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from mdtraj/formats/dcd/dcd.c:637: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ mdtraj/formats/dcd/dcd.c: In function ‘__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read’: mdtraj/formats/dcd/dcd.c:551:40: warning: ‘__pyx_v_i’ may be used uninitialized in this function [-Wmaybe-uninitialized] 551 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ mdtraj/formats/dcd/dcd.c:5280:7: note: ‘__pyx_v_i’ was declared here 5280 | int __pyx_v_i; | ^~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/mdtraj/formats/dcd/dcd.o build/temp.linux-x86_64-3.9/mdtraj/formats/dcd/src/dcdplugin.o -o /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/dcd.cpython-39-x86_64-linux-gnu.so building 'mdtraj.formats.binpos' extension creating build/temp.linux-x86_64-3.9/mdtraj/formats/binpos creating build/temp.linux-x86_64-3.9/mdtraj/formats/binpos/src x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/binpos/binpos.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/binpos/binpos.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from mdtraj/formats/binpos/binpos.c:637: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ mdtraj/formats/binpos/binpos.c: In function ‘__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read’: mdtraj/formats/binpos/binpos.c:5355:6: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 5355 | if (__pyx_t_2) { | ^ mdtraj/formats/binpos/binpos.c:4835:7: note: ‘__pyx_v_status’ was declared here 4835 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/binpos/binpos.c:551:40: warning: ‘__pyx_v_i’ may be used uninitialized in this function [-Wmaybe-uninitialized] 551 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ mdtraj/formats/binpos/binpos.c:4832:7: note: ‘__pyx_v_i’ was declared here 4832 | int __pyx_v_i; | ^~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/binpos/src/binposplugin.c -o build/temp.linux-x86_64-3.9/mdtraj/formats/binpos/src/binposplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/mdtraj/formats/binpos/binpos.o build/temp.linux-x86_64-3.9/mdtraj/formats/binpos/src/binposplugin.o -o /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/binpos.cpython-39-x86_64-linux-gnu.so building 'mdtraj.formats.dtr' extension creating build/temp.linux-x86_64-3.9/mdtraj/formats/dtr creating build/temp.linux-x86_64-3.9/mdtraj/formats/dtr/src x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-x86_64-3.9/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from mdtraj/formats/dtr/dtr.cpp:658: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-x86_64-3.9/mdtraj/formats/dtr/src/dtrplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/dtr/src/dtrplugin.cxx: In member function ‘bool desres::molfile::Timekeys::init(const string&)’: mdtraj/formats/dtr/src/dtrplugin.cxx:487:27: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %ld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx:487:40: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %ld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx: In constructor ‘{anonymous}::DDException::DDException(const string&, int)’: mdtraj/formats/dtr/src/dtrplugin.cxx:680:43: warning: ‘*.{anonymous}::DDException::eno’ is used uninitialized in this function [-Wuninitialized] 680 | : std::runtime_error(text + strerror(eno)), eno(_eno){} | ~~~~~~~~^~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘void DDmkdir(const string&, mode_t, int, int)’: mdtraj/formats/dtr/src/dtrplugin.cxx:706:16: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 706 | sprintf(sub, "%03x/", i); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:706:15: note: directive argument in the range [0, 2147483646] 706 | sprintf(sub, "%03x/", i); | ^~~~~~~ In file included from /usr/include/stdio.h:867, from mdtraj/formats/dtr/include/molfile_plugin.h:35, from mdtraj/formats/dtr/include/dtrplugin.hxx:46, from mdtraj/formats/dtr/src/dtrplugin.cxx:42: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10 bytes into a destination of size 6 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:714:23: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 714 | sprintf(subsub, "%03x", j); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:714:22: note: directive argument in the range [0, 2147483646] 714 | sprintf(subsub, "%03x", j); | ^~~~~~ In file included from /usr/include/stdio.h:867, from mdtraj/formats/dtr/include/molfile_plugin.h:35, from mdtraj/formats/dtr/include/dtrplugin.hxx:46, from mdtraj/formats/dtr/src/dtrplugin.cxx:42: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 4 and 9 bytes into a destination of size 6 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘std::string framefile(const string&, size_t, size_t, int, int)’: mdtraj/formats/dtr/src/dtrplugin.cxx:667:28: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 667 | sprintf(answer, "%03x/", d1); | ^ In file included from /usr/include/stdio.h:867, from mdtraj/formats/dtr/include/molfile_plugin.h:35, from mdtraj/formats/dtr/include/dtrplugin.hxx:46, from mdtraj/formats/dtr/src/dtrplugin.cxx:42: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10 bytes into a destination of size 9 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:665:28: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size between 0 and 5 [-Wformat-overflow=] 665 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:665:22: note: directive argument in the range [0, 2147483646] 665 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from mdtraj/formats/dtr/include/molfile_plugin.h:35, from mdtraj/formats/dtr/include/dtrplugin.hxx:46, from mdtraj/formats/dtr/src/dtrplugin.cxx:42: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 9 and 19 bytes into a destination of size 9 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/mdtraj/formats/dtr/dtr.o build/temp.linux-x86_64-3.9/mdtraj/formats/dtr/src/dtrplugin.o -o /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/dtr.cpython-39-x86_64-linux-gnu.so building 'mdtraj._rmsd' extension creating build/temp.linux-x86_64-3.9/mdtraj/rmsd creating build/temp.linux-x86_64-3.9/mdtraj/rmsd/src x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-x86_64-3.9/mdtraj/rmsd/_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/rmsd/_rmsd.cpp: In function ‘int __Pyx_InitGlobals()’: mdtraj/rmsd/_rmsd.cpp:24626:20: warning: ‘void PyEval_InitThreads()’ is deprecated [-Wdeprecated-declarations] 24626 | PyEval_InitThreads(); | ^ In file included from /usr/include/python3.9/Python.h:145, from mdtraj/rmsd/_rmsd.cpp:40: /usr/include/python3.9/ceval.h:130:37: note: declared here 130 | Py_DEPRECATED(3.9) PyAPI_FUNC(void) PyEval_InitThreads(void); | ^~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/center.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/rotation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/mdtraj/rmsd/_rmsd.o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/center.o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/rotation.o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/theobald_rmsd.o -lgomp -o /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/_rmsd.cpython-39-x86_64-linux-gnu.so building 'mdtraj._lprmsd' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-x86_64-3.9/mdtraj/rmsd/_lprmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from mdtraj/rmsd/_lprmsd.cpp:668: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ mdtraj/rmsd/_lprmsd.cpp: In function ‘int __Pyx_InitGlobals()’: mdtraj/rmsd/_lprmsd.cpp:9166:20: warning: ‘void PyEval_InitThreads()’ is deprecated [-Wdeprecated-declarations] 9166 | PyEval_InitThreads(); | ^ In file included from /usr/include/python3.9/Python.h:145, from mdtraj/rmsd/_lprmsd.cpp:48: /usr/include/python3.9/ceval.h:130:37: note: declared here 130 | Py_DEPRECATED(3.9) PyAPI_FUNC(void) PyEval_InitThreads(void); | ^~~~~~~~~~~~~~~~~~ mdtraj/rmsd/_lprmsd.cpp: In function ‘PyObject* __pyx_pf_6mdtraj_7_lprmsd_lprmsd(PyObject*, PyObject*, PyObject*, int, PyObject*, PyObject*, PyLongObject*, PyLongObject*)’: mdtraj/rmsd/_lprmsd.cpp:3964:14: warning: ‘__pyx_pybuffernd_ref_xyz_frame_dis.__Pyx_LocalBuf_ND::diminfo[0].__Pyx_Buf_DimInfo::shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 3964 | } else if (unlikely(__pyx_t_34 >= __pyx_pybuffernd_ref_xyz_frame_dis.diminfo[0].shape)) __pyx_t_33 = 0; | ^~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/Munkres.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/center.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/fancy_index.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/rotation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/mdtraj/rmsd/_lprmsd.o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/Munkres.o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/center.o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/fancy_index.o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/rotation.o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/theobald_rmsd.o -lgomp -o /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/_lprmsd.cpython-39-x86_64-linux-gnu.so building 'mdtraj.core.lib.libtheobald' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/theobald_rmsd.o -msse2 -mssse3 -O3 -funroll-loops x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/center.o -msse2 -mssse3 -O3 -funroll-loops x86_64-linux-gnu-gcc-ar rcs /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/lib/libtheobald.a build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/theobald_rmsd.o build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/center.o building 'mdtraj.geometry._geometry' extension creating build/temp.linux-x86_64-3.9/mdtraj/geometry creating build/temp.linux-x86_64-3.9/mdtraj/geometry/src x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/_geometry.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from mdtraj/geometry/src/_geometry.cpp:670: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ mdtraj/geometry/src/_geometry.cpp: In function ‘void __pyx_f_6mdtraj_8geometry_9_geometry_make_whole(__Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice)’: mdtraj/geometry/src/_geometry.cpp:5506:224: warning: ‘__pyx_v_delta[2]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 5506 | (__pyx_v_offset[__pyx_v_k]) = ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_8 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_7)) ))) * roundf(((__pyx_v_delta[2]) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_5 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_4)) )))))); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/geometry/src/_geometry.cpp:5520:277: warning: ‘__pyx_v_delta[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 5520 | (__pyx_v_offset[__pyx_t_9]) = ((__pyx_v_offset[__pyx_t_9]) + ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_4 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_5)) ))) * roundf((((__pyx_v_delta[1]) - (__pyx_v_offset[1])) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_7 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_8)) ))))))); | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ mdtraj/geometry/src/_geometry.cpp:5520:277: warning: ‘__pyx_v_offset[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/dssp.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/geometry.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/sasa.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/mdtraj/geometry/src/_geometry.o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/dssp.o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/geometry.o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/sasa.o -lgomp -o /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/_geometry.cpython-39-x86_64-linux-gnu.so building 'mdtraj.geometry.drid' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/drid.cpp -o build/temp.linux-x86_64-3.9/mdtraj/geometry/drid.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/geometry/drid.cpp: In function ‘int __Pyx_InitGlobals()’: mdtraj/geometry/drid.cpp:18465:20: warning: ‘void PyEval_InitThreads()’ is deprecated [-Wdeprecated-declarations] 18465 | PyEval_InitThreads(); | ^ In file included from /usr/include/python3.9/Python.h:145, from mdtraj/geometry/drid.cpp:39: /usr/include/python3.9/ceval.h:130:37: note: declared here 130 | Py_DEPRECATED(3.9) PyAPI_FUNC(void) PyEval_InitThreads(void); | ^~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/dridkernels.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/moments.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/mdtraj/geometry/drid.o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/dridkernels.o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/moments.o -lgomp -o /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/drid.cpython-39-x86_64-linux-gnu.so building 'mdtraj.geometry.neighbors' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-x86_64-3.9/mdtraj/geometry/neighbors.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/neighbors.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/mdtraj/geometry/neighbors.o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/neighbors.o -lgomp -o /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/neighbors.cpython-39-x86_64-linux-gnu.so building 'mdtraj.geometry.neighborlist' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-x86_64-3.9/mdtraj/geometry/neighborlist.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/neighborlist.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/geometry/src/neighborlist.cpp: In function ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’: mdtraj/geometry/src/neighborlist.cpp:50:53: warning: ‘periodicBoxVectors[0][0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 50 | periodicBoxSize[0] = periodicBoxVectors[0][0]; | ~~~~~~~~~~~~~~~~~~~~~~~^ mdtraj/geometry/src/neighborlist.cpp:51:53: warning: ‘periodicBoxVectors[1][1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 51 | periodicBoxSize[1] = periodicBoxVectors[1][1]; | ~~~~~~~~~~~~~~~~~~~~~~~^ mdtraj/geometry/src/neighborlist.cpp:52:53: warning: ‘periodicBoxVectors[2][2]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 52 | periodicBoxSize[2] = periodicBoxVectors[2][2]; | ~~~~~~~~~~~~~~~~~~~~~~~^ mdtraj/geometry/src/neighborlist.cpp:56:45: warning: ‘periodicBoxVectors[0][1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 56 | triclinic = (periodicBoxVectors[0][1] != 0.0 || periodicBoxVectors[0][2] != 0.0 || | ~~~~~~~~~~~~~~~~~~~~~~~^ x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/mdtraj-04fkzS/mdtraj-1.9.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/mdtraj/geometry/neighborlist.o build/temp.linux-x86_64-3.9/mdtraj/geometry/src/neighborlist.o -lgomp -o /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/neighborlist.cpython-39-x86_64-linux-gnu.so dh_auto_test -a -O--buildsystem=pybuild I: pybuild base:232: cd /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build; python3.9 -m unittest discover -v ---------------------------------------------------------------------- Ran 0 tests in 0.000s OK create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch --with python3,sphinxdoc --buildsystem=pybuild dh_testroot -a -O--buildsystem=pybuild dh_prep -a -O--buildsystem=pybuild dh_auto_install -a -O--buildsystem=pybuild I: pybuild base:232: /usr/bin/python3 setup.py install --root /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj Using built-in specs. COLLECT_GCC=/usr/bin/x86_64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/10/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa:hsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-10-Km9U7s/gcc-10-10.2.1/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-Km9U7s/gcc-10-10.2.1/debian/tmp-gcn/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-mutex Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20210110 (Debian 10.2.1-6) C compiler: Attempting to autodetect OpenMP support... Compiler supports OpenMP Attempting to autodetect SSE3 support... Compiler supports SSE3 Attempting to autodetect SSE4.1 support... Compiler supports SSE4.1 Attempting to autodetect NEON support... Did not detect NEON support running install running build running build_py copying mdtraj/version.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj running build_ext running install_lib creating /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj creating /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr creating /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib creating /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9 creating /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages creating /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj creating /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/nmr copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/nmr/__init__.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/nmr copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/nmr/shift_wrappers.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/nmr copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/nmr/scalar_couplings.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/nmr creating /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/nmr/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/nmr/__pycache__/shift_wrappers.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/nmr/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/nmr/__pycache__/scalar_couplings.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/nmr/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/nmr/__pycache__/__init__.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/nmr/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/__init__.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/_rmsd.cpython-39-x86_64-linux-gnu.so -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/_lprmsd.cpython-39-x86_64-linux-gnu.so -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj creating /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/testing copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/testing/testing.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/testing copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/testing/__init__.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/testing copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/testing/docstrings.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/testing copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/testing/docscrape.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/testing creating /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/testing/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/testing/__pycache__/testing.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/testing/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/testing/__pycache__/docscrape.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/testing/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/testing/__pycache__/__init__.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/testing/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/testing/__pycache__/docstrings.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/testing/__pycache__ creating /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters/netcdfreporter.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters/basereporter.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters/__init__.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters/xtcreporter.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters/dcdreporter.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters/hdf5reporter.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters creating /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters/__pycache__/hdf5reporter.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters/__pycache__/xtcreporter.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters/__pycache__/netcdfreporter.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters/__pycache__/dcdreporter.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters/__pycache__/basereporter.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/reporters/__pycache__/__init__.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters/__pycache__ creating /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils creating /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/baseunit.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/standard_dimensions.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/__init__.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/mymatrix.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/prefix.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/unit_math.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/doctests.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/constants.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/unit.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/unit_operators.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/quantity.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/unit_definitions.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/basedimension.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit creating /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/__pycache__/standard_dimensions.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/__pycache__/basedimension.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/__pycache__/baseunit.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/__pycache__/quantity.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/__pycache__/unit_definitions.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/__pycache__/prefix.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/__pycache__/mymatrix.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/__pycache__/__init__.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/__pycache__/unit.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unit/__pycache__/unit_operators.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/six.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/singleton.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/rotation.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/zipped.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/__init__.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/unitcell.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/contextmanagers.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/validation.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/delay_import.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils creating /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/__pycache__/rotation.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/__pycache__/six.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/__pycache__/delay_import.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/__pycache__/unitcell.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/__pycache__/validation.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/__pycache__/contextmanagers.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/__pycache__/__init__.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/__pycache__/singleton.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/utils/__pycache__/zipped.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/__pycache__ creating /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/residue_names.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/__init__.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core creating /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/lib copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/lib/libtheobald.a -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/lib copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/lib/center.h -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/lib copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/lib/theobald_rmsd.h -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/lib copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/topology.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/element.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/trajectory.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core creating /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/__pycache__/trajectory.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/__pycache__/selection.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/__pycache__/__init__.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/__pycache__/topology.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/__pycache__/residue_names.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/__pycache__/element.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/core/selection.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core creating /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/prmtop.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/trr.cpython-39-x86_64-linux-gnu.so -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/dcd.cpython-39-x86_64-linux-gnu.so -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/__init__.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/registry.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/mol2.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/hdf5.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/tng.cpython-39-x86_64-linux-gnu.so -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/psf.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/gro.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/lammpstrj.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/netcdf.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/amberrst.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/xtc.cpython-39-x86_64-linux-gnu.so -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/mdcrd.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/dtr.cpython-39-x86_64-linux-gnu.so -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/arc.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/openmmxml.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats creating /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/pdb copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb/pdbstructure.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/pdb copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb/__init__.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/pdb creating /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/pdb/data copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb/data/pdbNames.xml -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/pdb/data copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb/data/residues.xml -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/pdb/data copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb/pdbfile.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/pdb creating /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb/__pycache__/pdbfile.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb/__pycache__/pdbstructure.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/pdb/__pycache__/__init__.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/hoomdxml.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/xyzfile.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats creating /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/__pycache__/mol2.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/__pycache__/prmtop.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/__pycache__/amberrst.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/__pycache__/hdf5.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/__pycache__/hoomdxml.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/__pycache__/gro.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/__pycache__/xyzfile.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/__pycache__/gsd.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/__pycache__/psf.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/__pycache__/lammpstrj.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/__pycache__/arc.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/__pycache__/mdcrd.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/__pycache__/__init__.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/__pycache__/registry.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/__pycache__/lh5.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/__pycache__/openmmxml.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/__pycache__/netcdf.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/gsd.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/lh5.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/formats/binpos.cpython-39-x86_64-linux-gnu.so -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/io.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj creating /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/__pycache__/version.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/__pycache__/__init__.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/version.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj creating /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/contact.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/_geometry.cpython-39-x86_64-linux-gnu.so -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/__init__.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/sasa.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/dihedral.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/internal.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/alignment.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/dssp.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/thermodynamic_properties.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/angle.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/neighbors.cpython-39-x86_64-linux-gnu.so -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/neighborlist.cpython-39-x86_64-linux-gnu.so -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/shape.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/drid.cpython-39-x86_64-linux-gnu.so -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/rdf.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry creating /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/__pycache__/rg.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/__pycache__/rdf.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/__pycache__/hbond.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/__pycache__/sasa.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/__pycache__/angle.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/__pycache__/thermodynamic_properties.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/__pycache__/dihedral.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/__pycache__/shape.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/__pycache__/order.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/__pycache__/contact.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/__pycache__/dssp.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/__pycache__/distance.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/__pycache__/__init__.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/order.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/hbond.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/distance.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/geometry/rg.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry creating /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/scripts copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/scripts/__init__.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/scripts creating /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/scripts/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/scripts/__pycache__/__init__.cpython-39.pyc -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/scripts/__pycache__ copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/scripts/mdconvert.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/scripts copying /build/mdtraj-04fkzS/mdtraj-1.9.5/.pybuild/cpython3_3.9_mdtraj/build/mdtraj/scripts/mdinspect.py -> /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/scripts byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/nmr/__init__.py to __init__.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/nmr/shift_wrappers.py to shift_wrappers.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/nmr/scalar_couplings.py to scalar_couplings.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/__init__.py to __init__.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/testing/testing.py to testing.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/testing/__init__.py to __init__.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/testing/docstrings.py to docstrings.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/testing/docscrape.py to docscrape.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters/netcdfreporter.py to netcdfreporter.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters/basereporter.py to basereporter.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters/__init__.py to __init__.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters/xtcreporter.py to xtcreporter.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters/dcdreporter.py to dcdreporter.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/reporters/hdf5reporter.py to hdf5reporter.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/baseunit.py to baseunit.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/standard_dimensions.py to standard_dimensions.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/__init__.py to __init__.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/mymatrix.py to mymatrix.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/prefix.py to prefix.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/unit_math.py to unit_math.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/doctests.py to doctests.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/constants.py to constants.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/unit.py to unit.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/unit_operators.py to unit_operators.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/quantity.py to quantity.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/unit_definitions.py to unit_definitions.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unit/basedimension.py to basedimension.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/six.py to six.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/singleton.py to singleton.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/rotation.py to rotation.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/zipped.py to zipped.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/__init__.py to __init__.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/unitcell.py to unitcell.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/contextmanagers.py to contextmanagers.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/validation.py to validation.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/utils/delay_import.py to delay_import.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/residue_names.py to residue_names.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/__init__.py to __init__.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/topology.py to topology.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/element.py to element.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/trajectory.py to trajectory.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/core/selection.py to selection.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/prmtop.py to prmtop.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/__init__.py to __init__.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/registry.py to registry.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/mol2.py to mol2.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/hdf5.py to hdf5.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/psf.py to psf.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/gro.py to gro.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/lammpstrj.py to lammpstrj.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/netcdf.py to netcdf.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/amberrst.py to amberrst.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/mdcrd.py to mdcrd.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/arc.py to arc.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/openmmxml.py to openmmxml.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/pdb/pdbstructure.py to pdbstructure.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/pdb/__init__.py to __init__.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/pdb/pdbfile.py to pdbfile.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/hoomdxml.py to hoomdxml.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/xyzfile.py to xyzfile.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/gsd.py to gsd.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/formats/lh5.py to lh5.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/io.py to io.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/version.py to version.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/contact.py to contact.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/__init__.py to __init__.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/sasa.py to sasa.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/dihedral.py to dihedral.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/internal.py to internal.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/alignment.py to alignment.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/dssp.py to dssp.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/thermodynamic_properties.py to thermodynamic_properties.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/angle.py to angle.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/shape.py to shape.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/rdf.py to rdf.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/order.py to order.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/hbond.py to hbond.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/distance.py to distance.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/geometry/rg.py to rg.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/scripts/__init__.py to __init__.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/scripts/mdconvert.py to mdconvert.cpython-39.pyc byte-compiling /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj/scripts/mdinspect.py to mdinspect.cpython-39.pyc running install_egg_info running egg_info creating mdtraj.egg-info writing mdtraj.egg-info/PKG-INFO writing dependency_links to mdtraj.egg-info/dependency_links.txt writing entry points to mdtraj.egg-info/entry_points.txt writing requirements to mdtraj.egg-info/requires.txt writing top-level names to mdtraj.egg-info/top_level.txt writing manifest file 'mdtraj.egg-info/SOURCES.txt' reading manifest file 'mdtraj.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' no previously-included directories found matching '__pycache__' no previously-included directories found matching '*.pyc' writing manifest file 'mdtraj.egg-info/SOURCES.txt' Copying mdtraj.egg-info to /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/lib/python3.9/dist-packages/mdtraj-1.9.5.egg-info Skipping SOURCES.txt running install_scripts Installing mdconvert-mdtraj script to /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/bin Installing mdinspect script to /build/mdtraj-04fkzS/mdtraj-1.9.5/debian/python3-mdtraj/usr/bin dh_install -a -O--buildsystem=pybuild dh_installdocs -a -O--buildsystem=pybuild dh_sphinxdoc -a -O--buildsystem=pybuild dh_sphinxdoc: warning: Sphinx documentation not found dh_installchangelogs -a -O--buildsystem=pybuild dh_installexamples -a -O--buildsystem=pybuild dh_installman -a -O--buildsystem=pybuild dh_python3 -a -O--buildsystem=pybuild dh_installsystemduser -a -O--buildsystem=pybuild dh_perl -a -O--buildsystem=pybuild dh_link -a -O--buildsystem=pybuild dh_strip_nondeterminism -a -O--buildsystem=pybuild dh_compress -a -O--buildsystem=pybuild dh_fixperms -a -O--buildsystem=pybuild dh_missing -a -O--buildsystem=pybuild dh_dwz -a -a -O--buildsystem=pybuild dh_strip -a -a -O--buildsystem=pybuild dh_makeshlibs -a -a -O--buildsystem=pybuild dh_shlibdeps -a -a -O--buildsystem=pybuild dh_installdeb -a -O--buildsystem=pybuild dh_gencontrol -a -O--buildsystem=pybuild dpkg-gencontrol: warning: package python3-mdtraj: substitution variable ${python3:Provides} unused, but is defined dpkg-gencontrol: warning: package python3-mdtraj: substitution variable ${python3:Versions} unused, but is defined dpkg-gencontrol: warning: package python3-mdtraj: substitution variable ${python3:Provides} unused, but is defined dpkg-gencontrol: warning: package python3-mdtraj: substitution variable ${python3:Versions} unused, but is defined dh_md5sums -a -O--buildsystem=pybuild dh_builddeb -a -O--buildsystem=pybuild dpkg-deb: building package 'python3-mdtraj-dbgsym' in '../python3-mdtraj-dbgsym_1.9.5-1_amd64.deb'. dpkg-deb: building package 'python3-mdtraj' in '../python3-mdtraj_1.9.5-1_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../mdtraj_1.9.5-1_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-source: info: using options from mdtraj-1.9.5/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/mdtraj-04fkzS /tmp/mdtraj-1.9.5-1_3ftcfdj I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.jBkHI0i_TA... I: success in 792.1473 seconds md5: python3-mdtraj-dbgsym_1.9.5-1_amd64.deb: OK md5: python3-mdtraj_1.9.5-1_amd64.deb: OK sha1: python3-mdtraj-dbgsym_1.9.5-1_amd64.deb: OK sha1: python3-mdtraj_1.9.5-1_amd64.deb: OK sha256: python3-mdtraj-dbgsym_1.9.5-1_amd64.deb: OK sha256: python3-mdtraj_1.9.5-1_amd64.deb: OK Checksums: OK